phylogenetic tree of the DNA sequences from the ORF2 region. The reconstruction was performed on the cloned DNA sequences of the ORF2 region from the different populations of D. simulans and from some sequences detected in the sequenced genome (we eliminated sequences that were too short relative to the global length of the alignment). Colored boxes represent sequences harboring common patterns of deletions and/or insertions. All the positions are given relative to the complete copy. Green box:sequences display the same 4-bp deletion (at position 547) and the same 2-bp insertion (at position 112). Dark blue box: sequences display the same 1-bp deletion (at position 521). Yellow box: sequences display the same deletions of 3 bp (at position 143), 8 bp (at position 335), 4 bp (at position 345), and an insertion of 2 bp (at position 460). Light blue box: sequences display the same 401-bp deletion (at position 179). Orange box: sequences with no deletion or insertion, very closely related to the complete copy chr3R_1506433. Black asterisks correspond to bootstrap values greater than 50%.